USP49

Chr 6

ubiquitin specific peptidase 49

NCBI Gene: 25862ENSG00000164663UniProt: Q70CQ1

Enables histone binding activity and peptidase activity. Involved in mRNA splicing, via spliceosome; negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction; and protein deubiquitination. Predicted to be located in nucleoplasm. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
0
Active trials
13
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.35
LOEUF· LoF intol.
—
Mechanism
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.35LOEUF
pLI 0.938
Z-score 4.05
OE 0.15 (0.07–0.35)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
2.62Z-score
OE missense 0.64 (0.58–0.71)
271 obs / 422.6 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.15 (0.07–0.35)
0≤0.351.4
Missense OE?0.64 (0.58–0.71)
0≤0.61.4
Synonymous OE?0.97
0≤1.21.6
LoF obs/exp: 4 / 26.5Missense obs/exp: 271 / 422.6Syn Z: 0.37

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

USP49 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients